I am interested in identifying indels in whole genome bisulfite sequencing data (76bp paired end). Currently, I do this by setting the
-rdg affine gap penalty scores for bowtie2 to more permissive values than the default 5+3N and mapping using the bisulfite sequencing alignment wrapper, bismark.
My question is, what values of
-rdg will allow me to identify longest possible indels without sacrificing alignment quality? Is it better to set the affine penalty to zero with a high penalty for initially opening an indel (ex. 8+0N)? Or is it better to keep the initial penalty low and having a nonzero penalty for extension (ex. 2+1N)?